The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Open accessAbstract
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. Availability: http://samtools.sourceforge.net Contact: hengli@broadinstitute.org
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The Sequence Alignment/Map format and SAMtools
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Self-citationFast and accurate short read alignment with Burrows-Wheeler transform
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Self-citationA map of human genome variation from population-scale sequencing.
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Self-citationRecurring mutations found by sequencing an acute myeloid leukemia genome
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Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., et al. (2010) · Science · doi:10.1126/science.1190371 · Cited by 1,611
Genotype and SNP calling from next-generation sequencing data
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Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
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Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
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Variation in genome-wide mutation rates within and between human families
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Cited by
Haplotype-based variant detection from short-read sequencing
Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700
ANGSD: Analysis of Next Generation Sequencing Data
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Single-cell reconstruction of the early maternal–fetal interface in humans
Vento-Tormo, R., Efremova, M., Botting, R. A., Turco, M. Y., Vento-Tormo, M., Meyer, K. B., Park, J.-E., Stephenson, E., Polański, K., Goncalves, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0698-6 · Cited by 2,358
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Self-citationA chromosome conformation capture ordered sequence of the barley genome
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450
Self-citation
Metadata
- Authors
- Li, H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-09-08
- Volume
- 27
- Issue
- 21
- Pages
- 2987-2993
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2150131459
- Cited by
- 6,486
- References
- 13
- FWCI
- 15.64
- Type
- journal article
- Language
- en
- Open access
- green
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